Skip to main content
SpringerLink
Log in

Mitochondrial Genome and Plant Taxonomy

  • Protocol
  • First Online:
Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

The lability in size, structure, and sequence content of mitochondrial genome (mtDNA) across plant species has sharply limited its use in taxonomic studies. However, due to the new opportunities offered by the availability of complete mtDNA sequence in plant species and the subsequent development of universal primers, the number of mtDNA-based molecular studies has recently increased. Historically, universal primers have enabled to characterize mtDNA polymorphism mainly by the RFLP technique. This methodology has been progressively replaced by Sanger DNA sequencing, which actually provides the full phylogenetic information content of a DNA fragment (single nucleotide, insertion/deletion, and single sequence repeat length polymorphism). This chapter presents a sequencing working protocol to be routinely used in mtDNA-based phylogenetic studies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Gray MW, Burger G, Franz Lang B (2001) The origin and early evolution of mitochondria. Genome Biol 2:1018.1011–1018.1015

    Article  Google Scholar 

  2. Andersson SGE, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6:263–268

    Article  CAS  PubMed  Google Scholar 

  3. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu Y, Song K (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci USA 50:27–29

    Google Scholar 

  4. Adams KL, Daley DO, Qiu YL, Whelan J, Palmer JD (2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408:354–357

    Article  CAS  PubMed  Google Scholar 

  5. Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–395

    Article  CAS  PubMed  Google Scholar 

  6. Adams KL, Qiu YL, Stoutemyer M, Palmer JD (2002) Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 99:9905–9912

    Article  CAS  PubMed  Google Scholar 

  7. Boore JL (1999) Survey and summary. Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Bullerwell CE, Gray MW (2004) Evolution of the mitochondrial genome: protist connections to animals, fungi and plants. Curr Opin Microbiol 7:528–534

    Article  CAS  PubMed  Google Scholar 

  9. Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR (2012) Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol 10(1):e1001241

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Kitazaki K, Kubo T (2010) Cost of having the largest mitochondrial genome: evolutionary mechanism of plant mitochondrial genome. J Bot. doi:10.1155/2010/620137

    Google Scholar 

  11. Marienfeld J, Unseld M, Brennicke A (1999) The mitochondrial genome of Arabidopsis is composed of both native and immigrant information. Trends Plant Sci 4:495–502

    Article  PubMed  Google Scholar 

  12. Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8:5–14

    Article  CAS  PubMed  Google Scholar 

  13. Schuster W, Brennicke A (1994) The plant mitochondrial genome: physical structure, information content, RNA editing, and gene migration to the nucleus. Annu Rev Plant Physiol Plant Mol Biol 45:61–78

    Article  CAS  Google Scholar 

  14. Woloszynska M (2010) Heteroplasmy and stoichiometric complexity of plant mitochondrial genomes-though this be madness, yet there’s method in’t. J Exp Bot 61:657–671

    Article  CAS  PubMed  Google Scholar 

  15. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4:129–131

    Article  CAS  PubMed  Google Scholar 

  16. Duminil J, Pemonge MH, Petit RJ (2002) A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Mol Ecol Notes 2:428–430

    Article  CAS  Google Scholar 

  17. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058

    Article  CAS  PubMed  Google Scholar 

  18. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93:10274–10279

    Article  CAS  PubMed  Google Scholar 

  19. Muse SV (2000) Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol 42:25–43

    Article  CAS  PubMed  Google Scholar 

  20. Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, DePamphilis CW, Palmer JD (2005) Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol 5:1–12

    Article  Google Scholar 

  21. Cho Y, Mower JP, Qiu YL, Palmer JD (2004) Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci USA 101:17741–17746

    Article  CAS  PubMed  Google Scholar 

  22. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7:135

    Article  PubMed Central  PubMed  Google Scholar 

  23. Barr CM, Keller SR, Ingvarsson PK, Sloan DB, Taylor DR (2007) Variation in mutation rate and polymorphism among mitochondrial genes of Silene vulgaris. Mol Biol Evol 24:1783–1791

    Article  CAS  PubMed  Google Scholar 

  24. Birky CW Jr (2001) The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annu Rev Genet 35:125–148

    Article  CAS  PubMed  Google Scholar 

  25. Petit RJ, Vendramin GG (2007) Plant phylogeography based on organelle genes: an introduction. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European refugia: evolutionary perspectives on the origins and conservation of European biodiversity. Springer, Dordrecht, pp 23–101

    Chapter  Google Scholar 

  26. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701

    Article  CAS  PubMed  Google Scholar 

  27. Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T et al (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol 223:1–7

    Article  CAS  PubMed  Google Scholar 

  28. Marchelli P, Baier C, Mengel C, Ziegenhagen B, Gallo LA (2010) Biogeographic history of the threatened species Araucaria araucana (Molina) K. Koch and implications for conservation: a case study with organelle DNA markers. Conserv Genet 11:951–963

    Article  Google Scholar 

  29. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the Tortoise and the hare III. Am J Bot 94:275–288

    Article  CAS  PubMed  Google Scholar 

  30. Jeandroz S, Bastien D, Chandelier A, Du Jardin P, Favre JM (2002) A set of primers for amplification of mitochondrial DNA in Picea abies and other conifer species. Mol Ecol Notes 2:389–392

    Article  CAS  Google Scholar 

  31. Dumolin-Lapegue S, Pemonge MH, Petit RJ (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 6:393–397

    Article  CAS  PubMed  Google Scholar 

  32. Jaramillo-Correa JP, Bousquet J, Beaulieu J, Isabel N, Perron M, Bouillé M (2003) Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: The nature of polymorphism and variation within and among species in Picea. Theor Appl Genet 106:1353–1367

    CAS  PubMed  Google Scholar 

  33. Froelicher Y, Mouhaya W, Bassene JB, Costantino G, Kamiri M, Luro F, Morillon R, Ollitrault P (2011) New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny. Tree Genet Genomes 7:49–61

    Article  Google Scholar 

  34. Boonruangrod R, Desai D, Fluch S, Berenyi M, Burg K (2008) Identification of cytoplasmic ancestor gene-pools of Musa acuminata Colla and Musa balbisiana Colla and their hybrids by chloroplast and mitochondrial haplotyping. Theor Appl Genet 118:43–55

    Article  CAS  PubMed  Google Scholar 

  35. Godbout J, Jaramillo-Correa JP, Beaulieu J, Bousquet J (2005) A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Mol Ecol 14:3497–3512

    Article  CAS  PubMed  Google Scholar 

  36. Jaramillo-Correa JP, Beaulieu J, Bousquet J (2004) Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Mol Ecol 13:2735–2747

    Article  CAS  PubMed  Google Scholar 

  37. Jose-Maldia LS, Uchida K, Tomaru N (2009) Mitochondrial DNA variation in natural populations of Japanese larch (Larix kaempferi). Silvae Genetica 58:234–241

    Google Scholar 

  38. Naydenov K, Senneville S, Beaulieu J, Tremblay F, Bousquet J (2007) Glacial vicariance in Eurasia: Mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor. BMC Evol Biol 7:233

    Article  PubMed Central  PubMed  Google Scholar 

  39. Moriguchi Y, Kang KS, Lee KY, Lee SW, Kim YY (2009) Genetic variation of Picea jezoensis populations in South Korea revealed by chloroplast, mitochondrial and nuclear DNA markers. J Plant Res 122:153–160

    Article  CAS  PubMed  Google Scholar 

  40. Burban C, Petit RJ (2003) Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol Ecol 12:1487–1495

    Article  CAS  PubMed  Google Scholar 

  41. Bastien D, Favre JM, Collignon AM, Sperisen C, Jeandroz S (2003) Characterization of a mosaic minisatellite locus in the mitochondrial DNA of Norway spruce [Picea abies (L.) Karst.]. Theor Appl Genet 107:574–580

    Article  CAS  PubMed  Google Scholar 

  42. Yoshida Y, Matsunaga M, Cheng D, Xu D, Honma Y, Mikami T, Kubo T (2012) Mitochondrial minisatellite polymorphisms in fodder and sugar beets reveal genetic bottlenecks associated with domestication. Biologia Plantarum 56(2):369–372

    Google Scholar 

  43. Honma Y, Yoshida Y, Terachi T, Toriyama K, Mikami T, Kubo T (2011) Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica. Curr Genet 57:261–270

    Article  CAS  PubMed  Google Scholar 

  44. Fievet V, Touzet P, Arnaud JF, Cuguen J (2007) Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape the genetic structure? Mol Ecol 16:1847–1864

    Article  PubMed  Google Scholar 

  45. Sperisen C, Büchler U, Gugerli F, Mátyás G, Geburek T, Vendramin GG (2001) Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce. Mol Ecol 10:257–263

    Article  CAS  PubMed  Google Scholar 

  46. Lunt DH, Whipple LE, Hyman BC (1998) Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Mol Ecol 7:1441–1455

    Article  CAS  PubMed  Google Scholar 

  47. Nishizawa S, Kubo T, Mikami T (2000) Variable number of tandem repeat loci in the mitochondrial genomes of beets. Curr Genet 37:34–38

    Article  CAS  PubMed  Google Scholar 

  48. Hosaka K, Sanetomo R (2009) Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst 84:371–378

    Article  CAS  PubMed  Google Scholar 

  49. Avtzis DN, Aravanopoulos FA (2011) Host tree and insect genetic diversity on the borderline of natural distribution: a case study of Picea abies and Pityogenes chalcographus (Coleoptera, Scolytinae) in Greece. Silva Fennica 45:157–164

    Google Scholar 

  50. Gugger PF, Gonzalez-Rodriguez A, Rodriguez-Correa H, Sugita S, Cavender-Bares J (2011) Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of ‘rear edge’ populations. New Phytol 189:1185–1199

    Article  PubMed  Google Scholar 

  51. Jaramillo-Correa JP, Beaulieu J, Ledig FT, Bousquet J (2006) Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer. Mol Ecol 15:2787–2800

    Article  CAS  PubMed  Google Scholar 

  52. Goodall-Copestake WP, Pérez-Espona S, Harris DJ, Hollingsworth PM (2010) The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biol J Linn Soc 101:243–250

    Article  Google Scholar 

  53. Edwards EJ, Nyffeler R, Donoghue MJ (2005) Basal cactus phylogeny: implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form. Am J Bot 92:1177–1188

    Article  PubMed  Google Scholar 

  54. Eckert AJ, Tearse BR, Hall BD (2008) A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation. Mol Ecol 17:1983–1997

    Article  CAS  PubMed  Google Scholar 

  55. Cun YZ, Wang XQ (2010) Plant recolonization in the Himalaya from the southeastern Qinghai-Tibetan Plateau: geographical isolation contributed to high population differentiation. Mol Phylogenet Evol 56:972–982

    Article  CAS  PubMed  Google Scholar 

  56. Petrov DA, Hartl DL (2000) Pseudogene evolution and natural selection for a compact genome. J Hered 91(3):221–227

    Article  CAS  PubMed  Google Scholar 

  57. Duminil J, Grivet D, Ollier S, Jeandroz S, Petit RJ (2008) Multilevel control of organelle DNA sequence length in plants. J Mol Evol 66:405–415

    Article  CAS  PubMed  Google Scholar 

  58. Selosse MA, Albert B, Godelle B (2001) Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol Evol 16:135–141

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

Research funded by the FNRS (grants FRFC 2.4.576.07.F and MIS F.4.519.10.F). Many thanks to Michela Di Michele and Esra Kaymac for their comments on a previous version of the article.

Author information

Authors and Affiliations

  1. Service Evolution Biologique et Ecologie, CP160/12, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium

    Jérôme Duminil

  2. Biodiversity International, Forest Genetic Resources Programme, Sub-Regional Office for Central Africa, Yaoundé, Cameroon

    Jérôme Duminil

Authors
  1. Jérôme Duminil
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. UMR C53 PVBMT Université de la Réunion-Cirad, Université de la Réunion, Ile de la Réunion, France

    Pascale Besse

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer New York

About this protocol

Cite this protocol

Duminil, J. (2014). Mitochondrial Genome and Plant Taxonomy. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-767-9_6

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-766-2

  • Online ISBN: 978-1-62703-767-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation